AMBER Archive (2004)

Subject: Re: AMBER: Problems with xleap

From: Rhonda Torres (torres_at_scripps.edu)
Date: Mon Mar 01 2004 - 18:02:23 CST

Hi Xavi,

You could use the ambpdb functionality instead of ptraj to create
a pdb file.

Rhonda

Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

email: torres_at_scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896

On Thu, 26 Feb 2004, Javier Perez Miron wrote:

> Hi everyone!!
>
> I made an optimization in vacuum using SANDER.So, I obtained many files. One of
> them is the .rst file. I converted that .rst file into .pdb file using the
> ptraj program. After that, I want to load the .pdb file using xleap. I don't
> know why but xleap generate other new atoms.
>
> In xleap, I write the next lines:
>
> loadoff unit_name library.lib
> unit_name = loadpdb pdb_file.pdb
>
> and the program write the follow lines:
>
> Loading PDB file: ./file.pdb
> Unknown residue: HHH number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 1 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 2 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 3 type: Nonterminal
> Unknown residue: HHH number: 4 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 5 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 6 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> and then,
>
> Creating new UNIT for residue: HHH sequence: 1
> ...
> Creating new UNIT for residue: HHH sequence: 2
> ...
> Creating new UNIT for residue: HHH sequence: 3
> ...
> Creating new UNIT for residue: HHH sequence: 4
> ...
> Creating new UNIT for residue: HHH sequence: 5
> ...
> Creating new UNIT for residue: HHH sequence: 6
> ...
>
>
> How can I resolve this problem?
>
> Best regards,
>
>
> Xavi Perez
>
> Chemoinformatic
> Universitat Autonoma de Barcelona
> Barcelona, Spain.
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